| Filename | Total | Flagged As Poor Quality | Sequence Length | %GC |
|---|---|---|---|---|
| G1_KI_R1_clean.fq.gz | 9,633,848 | 0 | 30-150 | 45 |
| G1_KI_R2_clean.fq.gz | 9,633,848 | 0 | 30-150 | 45 |
| G1_KI_singletons_clean.fq.gz | 7,415,483 | 0 | 30-150 | 43 |
| G2_KI_R1_clean.fq.gz | 7,490,193 | 0 | 30-150 | 43 |
| G2_KI_R2_clean.fq.gz | 7,490,193 | 0 | 30-150 | 44 |
| G2_KI_singletons_clean.fq.gz | 9,151,523 | 0 | 30-150 | 43 |
| G3_KI_R1_clean.fq.gz | 6,247,947 | 0 | 30-150 | 44 |
| G3_KI_R2_clean.fq.gz | 6,247,947 | 0 | 30-150 | 44 |
| G3_KI_singletons_clean.fq.gz | 9,081,708 | 0 | 30-150 | 44 |
| G4_KI_R1_clean.fq.gz | 7,242,293 | 0 | 30-150 | 44 |
| G4_KI_R2_clean.fq.gz | 7,242,293 | 0 | 30-150 | 44 |
| G4_KI_singletons_clean.fq.gz | 8,661,390 | 0 | 30-150 | 45 |
| G5_KI_R1_clean.fq.gz | 5,731,056 | 0 | 30-150 | 43 |
| G5_KI_R2_clean.fq.gz | 5,731,056 | 0 | 30-150 | 43 |
| G5_KI_singletons_clean.fq.gz | 9,698,982 | 0 | 30-150 | 42 |
| G6K_CDNJBANXX_R1_clean.fq.gz | 70,903,097 | 0 | 30-125 | 45 |
| G6K_CDNJBANXX_R2_clean.fq.gz | 70,903,097 | 0 | 30-125 | 45 |
| G6K_CDNJBANXX_singletons_clean.fq.gz | 42,315 | 0 | 30-125 | 45 |
| G6T_CDNJBANXX_R1_clean.fq.gz | 68,246,684 | 0 | 30-125 | 47 |
| G6T_CDNJBANXX_R2_clean.fq.gz | 68,246,684 | 0 | 30-125 | 47 |
| G6T_CDNJBANXX_singletons_clean.fq.gz | 44,582 | 0 | 30-125 | 47 |
| G7K_CDNJBANXX_R1_clean.fq.gz | 73,079,277 | 0 | 30-125 | 46 |
| G7K_CDNJBANXX_R2_clean.fq.gz | 73,079,277 | 0 | 30-125 | 46 |
| G7K_CDNJBANXX_singletons_clean.fq.gz | 77,840 | 0 | 30-125 | 46 |
| G8_KI_R1_clean.fq.gz | 8,192,568 | 0 | 30-150 | 44 |
| G8_KI_R2_clean.fq.gz | 8,192,568 | 0 | 30-150 | 44 |
| G8_KI_singletons_clean.fq.gz | 8,723,253 | 0 | 30-150 | 44 |
Library Sizes ranged between 42,315 and 73,079,277 reads.
Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.
Summary of FastQC flags for each parameter
Heatmap showing mean base qualities for each library
Heatmap showing mean sequence qualities for each library
Heatmap of summed base distributions along each read
GC Content Heatmap normalised to theoretical GC content in the Hsapiens Transcriptome
GC Content Distributions for all reads showing theoretical GC content from the Hsapiens Transcriptome
Universal Adapter Content
Overrepresented_sequences missing from G1_KI_R2_clean.fq.gz Overrepresented_sequences missing from G4_KI_R2_clean.fq.gz Overrepresented_sequences missing from G8_KI_R2_clean.fq.gz Quitting from lines 188-189 (ngsReports_Fastqc.Rmd) Error: Aesthetics must be either length 1 or the same as the data (24): key
## Overrepresented_sequences missing from G1_KI_R2_clean.fq.gz
## Overrepresented_sequences missing from G4_KI_R2_clean.fq.gz
## Overrepresented_sequences missing from G8_KI_R2_clean.fq.gz
## `summarise()` regrouping output by 'Sequence' (override with `.groups` argument)
| Sequence | Total | Present In | Overall Percentage | Max_Percentage | Possible_Source |
|---|---|---|---|---|---|
| AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | 2,895,530 | 15 | 0.51118847% | 4.266778% | No Hit |
| GTCCGAAGGTGCAGCTACCACGGGCCTGGCCGCAAGCAAGTGTATCAGCA | 533,564 | 2 | 0.09419753% | 0.519317% | No Hit |
| CTCCCCTCTGCCCAGCATGTTTCCACATTCTACATTTCTAAGTGAATGGC | 504,275 | 2 | 0.08902673% | 0.475174% | No Hit |
| GTCAGACTTCTAGCTCTAGCAAGGACTCCTGCACTAAGCTTCAGCCATGA | 325,104 | 2 | 0.05739516% | 0.299131% | No Hit |
| CCGATGTTTTCAGAGGTGCCTCTGCATGGTCCGAAGGTGCAGCTACCACG | 301,849 | 2 | 0.05328963% | 0.261275% | No Hit |
| CAGACTTCTAGCTCTAGCAAGGACTCCTGCACTAAGCTTCAGCCATGAGG | 234,391 | 2 | 0.04138033% | 0.218089% | No Hit |
| GTGGAAAGAAGGTTAGGTTGACACCGGCAAATATGACGCCAAATTGAATT | 193,964 | 2 | 0.03424318% | 0.158729% | No Hit |
| GTCCCGATGTTTTCAGAGGTGCCTCTGCATGGTCCGAAGGTGCAGCTACC | 144,144 | 1 | 0.02544776% | 0.197243% | No Hit |
| GGGGATTCTATGGGGACTACTATGCGGTGATCTACTTCTAGCAGACGAAG | 131,053 | 1 | 0.02313662% | 0.179330% | No Hit |
| CTCGACGTCCGTGTCGCCTCCTGCGACGGCGACGACTGAGGCTGCGGCTC | 128,276 | 1 | 0.02264636% | 0.187959% | No Hit |
| CCTCGACGTCCGTGTCGCCTCCTGCGACGGCGACGACTGAGGCTGCGGCT | 118,522 | 1 | 0.02092435% | 0.173667% | No Hit |
| GGATCCTCTTCCTTCTCTTTACCATCTTTTTGGTCTTCTACCAAGCTGCT | 117,254 | 1 | 0.02070049% | 0.160448% | No Hit |
| CGATGTTTTCAGAGGTGCCTCTGCATGGTCCGAAGGTGCAGCTACCACGG | 115,112 | 1 | 0.02032233% | 0.157517% | No Hit |
| AGCCCATCAAGGACAGGTGGCGCTCCAGCTGCACAGAGCTCAAAAGGCAA | 108,354 | 1 | 0.01912925% | 0.158768% | No Hit |
| CGGGGAACTGCCAGGAGAAAAAGGATTGGCCATCAAGATGTAGGTTCTGG | 95,991 | 1 | 0.01694664% | 0.135383% | No Hit |
| CGGGGAACTGCCAGGAGAAAATGGATTGGCCATCAAGATGTAGGTTCTGG | 91,646 | 1 | 0.01617955% | 0.125406% | No Hit |
| GGGGATTGTTGATTTCGTCTATAAGATAAAGGATGCGGAGGGAGGGGAGG | 88,539 | 1 | 0.01563103% | 0.121155% | No Hit |
| GTTCGGCTTCCAAGACGCAGCATCACCAATCATAGAAGAGCTTTTACACT | 86,685 | 1 | 0.01530372% | 0.118618% | No Hit |
| GGACAGGTGGCGCTCCAGCTGCACAGAGCTCAAAAGGCAAAGCACCATCT | 82,994 | 1 | 0.01465209% | 0.121609% | No Hit |
| CCCACAGTAAACAGGAAAATAAAACCAAGAGCTCAGAGTATGGCAGCATC | 81,660 | 1 | 0.01441658% | 0.115171% | No Hit |
| CCCCTCTGCCCAGCATGTTTCCACATTCTACATTTCTAAGTGAATGGCTC | 79,546 | 1 | 0.01404337% | 0.108849% | No Hit |
| CTCCGACCGTGTCTGCGACCTCTTCTTCTGCCATGGCGCCTTCCCTTCTT | 75,185 | 1 | 0.01327346% | 0.110167% | No Hit |
| CCCCACAGTAAACAGGAAAATAAAACCAAGAGCTCAGAGTATGGCAGCAT | 71,370 | 1 | 0.01259995% | 0.100659% | No Hit |
| AACTTCCAGCTTCTCAGATATCTCATGGTCCTGGGCGTGCCCATTTGCAG | 68,170 | 4 | 0.01203501% | 0.248246% | No Hit |
| TTCTCAGATATCTCATGGTCCTGGGCGTGCCCATTTGCAGCAGCTGAGAG | 57,064 | 4 | 0.01007431% | 0.210368% | No Hit |
| TTCCAGCTTCTCAGATATCTCATGGTCCTGGGCGTGCCCATTTGCAGCAG | 54,223 | 4 | 0.00957275% | 0.198894% | No Hit |
| AGAAGTTGCAGGCAACTTCCAGCTTCTCAGATATCTCATGGTCCTGGGCG | 52,706 | 4 | 0.00930493% | 0.194512% | No Hit |
| AGGCAACTTCCAGCTTCTCAGATATCTCATGGTCCTGGGCGTGCCCATTT | 48,854 | 4 | 0.00862488% | 0.181133% | No Hit |
| GTGCCCATTTGCAGCAGCTGAGAGTTCCAAGTTGGCAGGTCCCGATGTTT | 37,798 | 3 | 0.00667301% | 0.175903% | No Hit |
| AGCTTCTCAGATATCTCATGGTCCTGGGCGTGCCCATTTGCAGCAGCTGA | 35,573 | 3 | 0.00628020% | 0.163604% | No Hit |
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale: LC_COLLATE=English_Australia.1252, LC_CTYPE=English_Australia.1252, LC_MONETARY=English_Australia.1252, LC_NUMERIC=C and LC_TIME=English_Australia.1252
attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: readr(v.1.4.0), stringr(v.1.4.0), magrittr(v.2.0.1), scales(v.1.1.1), pander(v.0.6.3), kableExtra(v.1.3.1), dplyr(v.1.0.0), ngsReports(v.1.2.0), tibble(v.3.0.1), ggplot2(v.3.3.2) and BiocGenerics(v.0.32.0)
loaded via a namespace (and not attached): bitops(v.1.0-6), matrixStats(v.0.57.0), lubridate(v.1.7.9.2), webshot(v.0.5.2), RColorBrewer(v.1.1-2), httr(v.1.4.2), GenomeInfoDb(v.1.22.1), tools(v.3.6.1), backports(v.1.2.0), R6(v.2.5.0), DT(v.0.17), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.3.0), tidyselect(v.1.1.0), compiler(v.3.6.1), cli(v.2.2.0), rvest(v.0.3.6), Biobase(v.2.46.0), flashClust(v.1.01-2), xml2(v.1.3.2), DelayedArray(v.0.12.3), plotly(v.4.9.3), ggdendro(v.0.1.22), labeling(v.0.4.2), checkmate(v.2.0.0), digest(v.0.6.25), Rsamtools(v.2.2.3), rmarkdown(v.2.6), XVector(v.0.26.0), jpeg(v.0.1-8.1), pkgconfig(v.2.0.3), htmltools(v.0.5.0), highr(v.0.8), FactoMineR(v.2.4), htmlwidgets(v.1.5.3), rlang(v.0.4.11), rstudioapi(v.0.13), farver(v.2.0.3), generics(v.0.1.0), zoo(v.1.8-8), hwriter(v.1.3.2), jsonlite(v.1.7.1), crosstalk(v.1.1.0.1), BiocParallel(v.1.20.1), RCurl(v.1.98-1.2), GenomeInfoDbData(v.1.2.2), leaps(v.3.1), Matrix(v.1.2-18), fansi(v.0.4.1), Rcpp(v.1.0.5), munsell(v.0.5.0), S4Vectors(v.0.24.4), lifecycle(v.0.2.0), scatterplot3d(v.0.3-41), stringi(v.1.4.6), yaml(v.2.2.1), MASS(v.7.3-51.6), SummarizedExperiment(v.1.16.1), zlibbioc(v.1.32.0), plyr(v.1.8.6), grid(v.3.6.1), ggrepel(v.0.9.0), crayon(v.1.3.4), lattice(v.0.20-41), Biostrings(v.2.54.0), hms(v.0.5.3), knitr(v.1.29), pillar(v.1.4.7), GenomicRanges(v.1.38.0), reshape2(v.1.4.4), stats4(v.3.6.1), glue(v.1.4.1), evaluate(v.0.14), ShortRead(v.1.44.3), latticeExtra(v.0.6-29), data.table(v.1.13.6), vctrs(v.0.3.1), png(v.0.1-7), gtable(v.0.3.0), purrr(v.0.3.4), tidyr(v.1.1.2), assertthat(v.0.2.1), xfun(v.0.15), viridisLite(v.0.3.0), truncnorm(v.1.0-8), GenomicAlignments(v.1.22.1), IRanges(v.2.20.2), cluster(v.2.1.0) and ellipsis(v.0.3.1)